By Gordon Corera
BBC Security Correspondent
"Gary, your orders are to find Bin Laden and his lieutenants, kill them and bring Bin Laden's head back to the United States in a cardboard box on dry ice."
'Extraordinary rendition' of terror suspects is part of new CIA tactics
Those instructions, given to agent Gary Schroen by Cofer Black, Director of the CIA's Counter Terrorist Center, two days after 11 September 2001, sent a clear message: things had changed for the Central Intelligence Agency.
Where in the 1990s, lawyers argued over whether the CIA could target Bin Laden directly for death rather than capture, now the restraints had come off.
In its 60-year history, the CIA has undergone periodic spasms and convulsions, waves of aggressive activity followed by retreat and a drawing back. But tensions remained between two of its functions - how far was it an intelligence gathering agency, and how far was it the covert arm of American presidential power?
9/11 had been full of confusion at CIA headquarters in Langley, Virginia.
After watching transfixed as events unfolded on their TV screens, most staff were told to evacuate the building and go home in case they too were a target for al-Qaeda. Many of them found themselves milling around in the car park as the roads around Langley jammed with traffic.
For some officers it was a chance to reflect - wasn't this exactly the kind of event the CIA was supposed to stop? The next day, a tired-looking CIA director George Tenet addressed staff in the agency's auditorium.
CIA director George Tenet stepped down in 2004
Whatever the past was, the agency now had a clear mission and it was going to pursue it relentlessly. It would defeat al-Qaeda.
The emotions were complex. Amongst some, there was anger that previous opportunities to take out Osama Bin Laden has been missed.
"In a very parochial sense, I also thought the agency would get blamed for it," explains Mike Scheuer, who ran the CIA's team to track down Bin Laden from in the late 1990s.
Other officers felt the adrenalin rush at being finally being given the authority to do whatever it took.
"My personal emotion was, 'it is now officially started'," recalls Cofer Black, who would be charged with planning the initial campaign against al-Qaeda.
"The analogy would be the junkyard dog that had been chained to the ground was now going to be let go. And I just couldn't wait."
After a series of major scandals in the 1970s, the CIA had been hauled through the coals by Congress and told to clean up its act.
Assassination was formally banned, and anything that could bring on a career-ending congressional investigation was discouraged.
The attack on the Twin Towers and the Pentagon changed that. Cofer Black would later tell Congress after 11 September, "the gloves came off."
Four-and-a-half years later, the way in which that new, more aggressive CIA began to operate is only now becoming clear. And with it has come a growing backlash.
As the CIA's tough tactics come under growing scrutiny, even allies closest to the US are having to publicly distance themselves from its operations - even if they know far more about them than they are letting on.
As well as a less rigid line on assassinating al-Qaeda's leaders, there would also be more relaxed rules, issued at the highest levels, about what kind of "techniques" could be used by the CIA in interrogating al-Qaeda detainees, some of whom became "ghost prisoners" at secret locations.
The US missile attack in Pakistan prompted outrage in the country
In Europe, concerns would grow over how these prisoners were transported. The Romanian foreign minister denied his country had ever housed prisoners, but defended the need to co-operate with the US, despite all the controversy it creates.
"As for the flights, they happen. There is a cooperation between our intelligence services and it does a lot of good," he explained.
Co-operation with allies is vital, but the CIA is becoming so controversial in many countries that they are forced to distance themselves if that co-operation becomes public or goes awry.
That has been the case when it comes to rendition not only in Europe but also in Pakistan, where the government quickly distanced themselves from a CIA strike in its Bajur province in January.
The strike was targeting al-Qaeda's number two, but protests erupted in the country.
"Pakistan had no idea that the air-strike was going to take place," Pakistan's Prime Minister, Shaukat Aziz, told the BBC.
"Any action in our territory must be conducted by Pakistan forces."
The tactics of the CIA are coming increasingly under the spotlight and the subject of public debate. Who ordered them? Are they morally acceptable? How far are they essential tools in the fight against the most committed of opponents?
Or are they becoming counter-productive, undermining claims to the moral high-ground as well as international alliances vital to the US war on terror?
Secret Wars: The CIA After 9/11 is broadcast on BBC World Service on Monday 13 March at 0906 GMT.